[gmx-users] Multiple runs for same system
jalemkul at vt.edu
Mon Feb 26 00:09:46 CET 2018
On 2/25/18 6:07 PM, Dr. Seema Mishra wrote:
> Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. Right?
However you want to do it, either by specifying a seed or letting grompp
generate one. Some prefer the former for reproducibility, but given all
the things that can affect binary reproducibility, I don't think it's a
> After this, how many runs will be performed? One? Then after the production run is finished, start it again with gen_seed=-1 for the second run?
Each .tpr specifies one initial set of conditions for a simulation. If
you want another simulation, generate another .tpr that specifies a
different set of conditions.
> This is to be done for 3 independent runs for same protein-ligand system.
> On Monday, 26 February 2018 4:16 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> Multiple runs are typically initiated simply by changing gen_seed when
> generating velocities at the outset of equilibration.
> As for clustering, you'll have to explain what you mean. Clustering
> ligand poses? Protein? What? Does a Google search for "GROMACS
> clustering" or the help information for gmx cluster point you to
> anything useful
> On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:
>> Or just direct me to the steps written anywhere....
>> On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra <seema_uoh at yahoo.com> wrote:
>> Hi, Can anyone tell me the steps and commands for performing multiple runs of 50 ns for same protein-ligand system? Also the clustering for further analyses. Thanks.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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